Cenozoic climatic and environmental changes in the arid Asian interior, and their possible relations with global climatic changes and the Tibetan Plateau uplift, have been intensively investigated and debated over past decades. Here we present 40-Myr (million years)-long n-alkane records from a continuous Cenozoic sediment sequence in the Dahonggou Section, Qaidam Basin, northern Tibetan Plateau, to infer environmental changes in the northern basin. A set of n-alkane indexes, including ACL, CPI and Paq, vary substantially and consistently throughout the records, which are interpreted to reflect relative contributions from terrestrial vascular plants vs. aquatic macrophytes, and thus indicate depositional environments. ACL values vary between 21 and 30; CPI values range from 1.0 to 8.0; and Paq values change from <0.1 to 0.8 over the past 40-Myr. We have roughly identified two periods, at 25.8–21.0 Ma (million years ago) and 13.0–17.5 Ma, with higher ACL and CPI and lower Paq values indicating predominant lacustrine environments. Lower ACL and CPI values, together with higher Paq values, occurred at >25.8 Ma, 17.5–21.0 Ma, and <13.0 Ma, corresponding to alluvial fan/river deltaic deposits and shallow lacustrine settings, consistent with the observed features in sedimentological facies. The inferred Cenozoic environmental changes in the northern Qaidam Basin appear to correspond to global climatic changes.